Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/python-cogent/python-cogent_2021.10.12a1+dfsg-1_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/python-cogent-2021.10.12a1+dfsg-11053bbjh/python-cogent_2021.10.12a1+dfsg-1_all.buildinfo Get source package info: python-cogent=2021.10.12a1+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/python-cogent/2021.10.12a1+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3.1 binfmt-support=2.2.1-1 binutils=2.37-8 binutils-common=2.37-8 binutils-x86-64-linux-gnu=2.37-8 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20211016 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-10 cython3=0.29.24-1 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-python=5.20211022.1 dh-strip-nondeterminism=1.12.0-2 diffutils=1:3.7-5 docutils-common=0.17.1+dfsg-2 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 flit=3.0.0-1 fonts-lyx=2.3.6-1 g++=4:11.2.0-2 g++-11=11.2.0-10 gcc=4:11.2.0-2 gcc-11=11.2.0-10 gcc-11-base=11.2.0-10 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-10 libatomic1=11.2.0-10 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1 libbinutils=2.37-8 libblas3=3.10.0-1 libblkid1=2.37.2-4 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-10 libcmark-gfm-extensions0=0.29.0.gfm.0-6 libcmark-gfm0=0.29.0.gfm.0-6 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.25-2 libcrypt1=1:4.4.25-2 libctf-nobfd0=2.37-8 libctf0=2.37-8 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.5.2 libdeflate0=1.8-1 libdpkg-perl=1.20.9 libedit2=3.1-20210910-1 libelf1=0.185-2 libexpat1=2.4.1-3 libexpat1-dev=2.4.1-3 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.0-2 libfreetype6=2.11.0+dfsg-1 libfribidi0=1.0.8-2 libgcc-11-dev=11.2.0-10 libgcc-s1=11.2.0-10 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgfortran5=11.2.0-10 libglib2.0-0=2.70.0-3 libgmp10=2:6.2.1+dfsg-2 libgomp1=11.2.0-10 libgpg-error0=1.42-3 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-7 libharfbuzz0b=2.7.4-1 libicu67=67.1-7 libimagequant0=2.12.2-1.1 libisl23=0.24-2 libitm1=11.2.0-10 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:2.0.6-4 libjs-jquery=3.5.1+dfsg+~3.5.5-8 libjs-jquery-ui=1.12.1+dfsg-8 libjs-sphinxdoc=4.2.0-5 libjs-underscore=1.9.1~dfsg-4 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblapack3=3.10.0-1 liblbfgsb0=3.0+dfsg.3-9 liblcms2-2=2.12~rc1-2 libllvm9=1:9.0.1-20 liblsan0=11.2.0-10 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.4-1 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.2+20210905-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libopenjp2-7=2.4.0-3 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpfm4=4.11.1+git32-gd0b85fb-1 libpipeline1=1.5.3-1 libpng16-16=1.6.37-3 libpython3-all-dev=3.9.7-1 libpython3-dev=3.9.7-1 libpython3-stdlib=3.9.7-1 libpython3.9=3.9.7-4 libpython3.9-dev=3.9.7-4 libpython3.9-minimal=3.9.7-4 libpython3.9-stdlib=3.9.7-4 libquadmath0=11.2.0-10 libraqm0=0.7.0-4 libreadline8=8.1-2 libseccomp2=2.5.2-2 libselinux1=3.1-3+b1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libsqlite3-0=3.36.0-2 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-10 libstdc++6=11.2.0-10 libsub-override-perl=0.09-2 libsystemd0=249.5-2 libtbb2=2020.3-1 libtiff5=4.3.0-2 libtinfo6=6.2+20210905-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-10 libubsan1=11.2.0-10 libuchardet0=0.0.7-1 libudev1=249.5-2 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libwebp6=0.6.1-2.1 libwebpdemux2=0.6.1-2.1 libwebpmux3=0.6.1-2.1 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxml2=2.9.12+dfsg-5 libz3-4=4.8.12-1+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.14.12-1 llvm-9=1:9.0.1-20 llvm-9-runtime=1:9.0.1-20 login=1:4.8.1-1.1 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.70 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 ncurses-base=6.2+20210905-1 ncurses-bin=6.2+20210905-1 openssl=1.1.1l-1 pandoc=2.9.2.1-1+b2 pandoc-data=2.9.2.1-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 python-babel-localedata=2.8.0+dfsg.1-7 python-matplotlib-data=3.3.4-2 python3=3.9.7-1 python3-alabaster=0.7.12-1 python3-all=3.9.7-1 python3-all-dev=3.9.7-1 python3-attr=20.3.0-1 python3-babel=2.8.0+dfsg.1-7 python3-bleach=4.1.0-1 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-cycler=0.11.0-1 python3-dateutil=2.8.1-6 python3-decorator=4.4.2-2 python3-defusedxml=0.7.1-1 python3-dev=3.9.7-1 python3-distutils=3.9.7-1 python3-docutils=0.17.1+dfsg-2 python3-entrypoints=0.3-8 python3-html5lib=1.1-3 python3-idna=2.10-1 python3-imagesize=1.2.0-2 python3-importlib-metadata=4.6.4-1 python3-iniconfig=1.1.1-1 python3-ipython-genutils=0.2.0-5 python3-jinja2=3.0.1-2 python3-jsonschema=3.2.0-3 python3-jupyter-core=4.9.1-1 python3-kiwisolver=1.3.2-1 python3-lib2to3=3.9.7-1 python3-llvmlite=0.35.0-3 python3-markupsafe=2.0.1-2 python3-matplotlib=3.3.4-2 python3-minimal=3.9.7-1 python3-mistune=0.8.4-5 python3-more-itertools=4.2.0-3 python3-nbconvert=5.6.1-3 python3-nbformat=5.1.3-1 python3-nbsphinx=0.8.7+ds-1 python3-numba=0.52.0-5 python3-numpy=1:1.19.5-1 python3-numpydoc=1.1.0-3 python3-packaging=21.0-1 python3-pandas=1.1.5+dfsg-2 python3-pandas-lib=1.1.5+dfsg-2 python3-pandocfilters=1.4.3-1 python3-pil=8.3.2-1 python3-pkg-resources=58.2.0-1 python3-pluggy=0.13.0-7.1 python3-py=1.10.0-1 python3-pygments=2.7.1+dfsg-2.1 python3-pyparsing=2.4.7-1 python3-pyrsistent=0.15.5-1+b3 python3-pytest=6.2.5-1 python3-pytoml=0.1.21-1 python3-requests=2.25.1+dfsg-2 python3-roman=3.3-1 python3-scipy=1.7.1-1 python3-scitrack=2021.5.3-1 python3-setuptools=58.2.0-1 python3-six=1.16.0-2 python3-snowballstemmer=2.1.0-2 python3-sphinx=4.2.0-5 python3-sphinx-bootstrap-theme=0.8.0-1 python3-sphinx-gallery=0.10.0-1 python3-testpath=0.5.0+dfsg-1 python3-tinydb=3.15.2-2 python3-toml=0.10.2-1 python3-tqdm=4.57.0-2 python3-traitlets=5.1.1-1 python3-tz=2021.3-1 python3-urllib3=1.26.5-1~exp1 python3-webencodings=0.5.1-4 python3-zipp=1.0.0-3 python3.9=3.9.7-4 python3.9-dev=3.9.7-4 python3.9-minimal=3.9.7-4 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 sphinx-common=4.2.0-5 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 ttf-bitstream-vera=1.10-8.1 tzdata=2021e-1 util-linux=2.37.2-4 xml-core=0.18+nmu1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211104T150851Z/ unstable main deb-src http://snapshot.notset.fr/archive/debian/20211104T150851Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220421T153504Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211103T204712Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d python-cogent=2021.10.12a1+dfsg-1 && mkdir -p /build/python-cogent-zLCQYQ && dpkg-source --no-check -x /*.dsc /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg && chown -R builduser:builduser /build/python-cogent-zLCQYQ" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1636014544" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/python-cogent-zLCQYQ /tmp/python-cogent-2021.10.12a1+dfsg-11053bbjh bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211103T204712Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.iZ1LuJvRjE as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.iZ1LuJvRjE Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211103T204712Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211103T204712Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (577 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4664 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211104T150851Z/ unstable main deb-src http://snapshot.notset.fr/archive/debian/20211104T150851Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220421T153504Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211103T204712Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.iZ1LuJvRjE Get:1 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable InRelease [165 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220421T153504Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211103T204712Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main Sources [12.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main amd64 Packages [11.9 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220421T153504Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220421T153504Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220421T153504Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220421T153504Z unstable/main amd64 Packages [12.4 MB] Fetched 37.0 MB in 30s (1216 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.iZ1LuJvRjE I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d python-cogent=2021.10.12a1+dfsg-1 && mkdir -p /build/python-cogent-zLCQYQ && dpkg-source --no-check -x /*.dsc /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg && chown -R builduser:builduser /build/python-cogent-zLCQYQ"' exec /tmp/mmdebstrap.iZ1LuJvRjE Reading package lists... NOTICE: 'python-cogent' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-cogent.git Please use: git clone https://salsa.debian.org/med-team/python-cogent.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3027 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main python-cogent 2021.10.12a1+dfsg-1 (dsc) [2572 B] Get:2 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main python-cogent 2021.10.12a1+dfsg-1 (tar) [3013 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main python-cogent 2021.10.12a1+dfsg-1 (diff) [11.6 kB] Fetched 3027 kB in 2s (1262 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'python-cogent_2021.10.12a1+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting python-cogent in /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg dpkg-source: info: unpacking python-cogent_2021.10.12a1+dfsg.orig.tar.xz dpkg-source: info: unpacking python-cogent_2021.10.12a1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sphinx.patch dpkg-source: info: applying fix_interpreter.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1636014544" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.iZ1LuJvRjE dpkg-buildpackage: info: source package python-cogent dpkg-buildpackage: info: source version 2021.10.12a1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg' #These files are rebuilt on-the-fly for f in `find -name '*.c'` ; do \ head -n 1 "$f" | grep -q '^/\* Generated by Cython' && rm "$f" ; \ done rm -rf build build-stamp rm -rf doc/_build dh_clean make[1]: Leaving directory '/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg' debian/rules binary-indep dh binary-indep --with python3 --buildsystem=pybuild dh_update_autotools_config -i -O--buildsystem=pybuild dh_autoreconf -i -O--buildsystem=pybuild dh_auto_configure -i -O--buildsystem=pybuild debian/rules override_dh_auto_build make[1]: Entering directory '/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg' dh_auto_build I: pybuild plugin_flit:66: Installing package /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/src/cogent3 -> /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3 I: pybuild plugin_flit:79: Writing dist-info /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/ set -x; cd doc; PYTHONPATH=/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg http_proxy='127.0.0.1:9' /usr/bin/make html + cd doc + PYTHONPATH=/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg http_proxy=127.0.0.1:9 /usr/bin/make html make[2]: Entering directory '/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v4.2.0 making output directory... done WARNING: html_static_path entry '_static' does not exist WARNING: The config value `today' has type `date', defaults to `str'. [autosummary] generating autosummary for: api/__init__/cogent3.__init__.available_apps.rst, api/__init__/cogent3.__init__.available_codes.rst, api/__init__/cogent3.__init__.available_models.rst, api/__init__/cogent3.__init__.available_moltypes.rst, api/__init__/cogent3.__init__.get_code.rst, api/__init__/cogent3.__init__.get_model.rst, api/__init__/cogent3.__init__.get_moltype.rst, api/__init__/cogent3.__init__.load_aligned_seqs.rst, api/__init__/cogent3.__init__.load_delimited.rst, api/__init__/cogent3.__init__.load_table.rst, ..., examples/scope_model_params_on_trees.rst, examples/seq_features.rst, examples/simple.rst, examples/simulate_alignment.rst, examples/testing_multi_loci.rst, general.rst, index.rst, install.rst, licenses.rst, pycogent.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 110 source files that are out of date updating environment: [new config] 110 added, 0 changed, 0 removed reading sources... [ 0%] api/__init__/cogent3.__init__.available_apps reading sources... [ 1%] api/__init__/cogent3.__init__.available_codes reading sources... [ 2%] api/__init__/cogent3.__init__.available_models reading sources... [ 3%] api/__init__/cogent3.__init__.available_moltypes reading sources... [ 4%] api/__init__/cogent3.__init__.get_code reading sources... [ 5%] api/__init__/cogent3.__init__.get_model reading sources... [ 6%] api/__init__/cogent3.__init__.get_moltype reading sources... [ 7%] api/__init__/cogent3.__init__.load_aligned_seqs reading sources... [ 8%] api/__init__/cogent3.__init__.load_delimited reading sources... [ 9%] api/__init__/cogent3.__init__.load_table reading sources... [ 10%] api/__init__/cogent3.__init__.load_tree reading sources... [ 10%] api/__init__/cogent3.__init__.load_unaligned_seqs reading sources... [ 11%] api/__init__/cogent3.__init__.make_aligned_seqs reading sources... [ 12%] api/__init__/cogent3.__init__.make_seq reading sources... [ 13%] api/__init__/cogent3.__init__.make_table reading sources... [ 14%] api/__init__/cogent3.__init__.make_tree reading sources... [ 15%] api/__init__/cogent3.__init__.make_unaligned_seqs reading sources... [ 16%] api/alignment/alignment reading sources... [ 17%] api/alignment/classes/cogent3.core.alignment.Alignment reading sources... [ 18%] api/alignment/classes/cogent3.core.alignment.ArrayAlignment reading sources... [ 19%] api/alignment/classes/cogent3.core.alignment.SequenceCollection reading sources... [ 20%] api/alphabet/alphabet reading sources... [ 20%] api/alphabet/classes/cogent3.core.alphabet.Alphabet reading sources... [ 21%] api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode reading sources... [ 22%] api/genetic_code/genetic_code reading sources... [ 23%] api/index reading sources... [ 24%] api/moltype/classes/cogent3.core.moltype.MolType reading sources... [ 25%] api/moltype/moltype reading sources... [ 26%] api/sequence/classes/cogent3.core.sequence.DnaSequence reading sources... [ 27%] api/sequence/classes/cogent3.core.sequence.ProteinSequence reading sources... [ 28%] api/sequence/classes/cogent3.core.sequence.RnaSequence reading sources... [ 29%] api/sequence/sequence reading sources... [ 30%] api/table/classes/cogent3.parse.table.FilteringParser reading sources... [ 30%] api/table/classes/cogent3.util.table.Columns reading sources... [ 31%] api/table/classes/cogent3.util.table.Table reading sources... [ 32%] api/table/table reading sources... [ 33%] api/tree/classes/cogent3.core.tree.PhyloNode reading sources... [ 34%] api/tree/tree reading sources... [ 35%] app/align-codon reading sources... [ 36%] app/align-nucleotide reading sources... [ 37%] app/align-protein reading sources... [ 38%] app/app-overview reading sources... [ 39%] app/available-apps reading sources... [ 40%] app/dstore reading sources... [ 40%] app/evo-ancestral-states reading sources... [ 41%] app/evo-dt-nuc-model reading sources... [ 42%] app/evo-extract-model-stats reading sources... [ 43%] app/evo-hypothesis reading sources... [ 44%] app/evo-model reading sources... [ 45%] app/evo-model-timehet reading sources... [ 46%] app/evo-model-with-tree reading sources... [ 47%] app/evo-natsel_neutral reading sources... [ 48%] app/evo-natsel_sitehet reading sources... [ 49%] app/evo-natsel_timehet reading sources... [ 50%] app/evo-natsel_zhang reading sources... [ 50%] app/evo-nstat-codon-model reading sources... [ 51%] app/evo-tr-codon-model reading sources... [ 52%] app/evo-tr-nuc-model reading sources... [ 53%] app/index reading sources... [ 54%] app/not-completed reading sources... [ 55%] app/user_function reading sources... [ 56%] app/warning reading sources... [ 57%] cookbook/DNA_and_RNA_sequences reading sources... [ 58%] cookbook/alignments reading sources... [ 59%] cookbook/alphabet reading sources... [ 60%] cookbook/annotations reading sources... [ 60%] cookbook/building_alignments reading sources... [ 61%] cookbook/building_phylogenies reading sources... [ 62%] cookbook/calc_genetic_distance reading sources... [ 63%] cookbook/evo_modelling reading sources... [ 64%] cookbook/genetic_code reading sources... [ 65%] cookbook/index reading sources... [ 66%] cookbook/loading_sequences reading sources... [ 67%] cookbook/loading_tabular reading sources... [ 68%] cookbook/manipulating_biological_data reading sources... [ 69%] cookbook/moltypes reading sources... [ 70%] cookbook/protein_sequences reading sources... [ 70%] cookbook/simple_trees reading sources... [ 71%] cookbook/tables reading sources... [ 72%] cookbook/useful_utilities reading sources... [ 73%] cookbook/what_codes reading sources... [ 74%] data_file_links reading sources... [ 75%] examples/align_codons_to_protein reading sources... [ 76%] examples/calculate_UPGMA_cluster reading sources... [ 77%] examples/calculate_neigbourjoining_tree reading sources... [ 78%] examples/calculate_pairwise_distances reading sources... [ 79%] examples/codon_models reading sources... [ 80%] examples/coevolution reading sources... [ 80%] examples/complete_seq_features reading sources... [ 81%] examples/empirical_protein_models reading sources... [ 82%] examples/hmm_par_heterogeneity reading sources... [ 83%] examples/index reading sources... [ 84%] examples/manipulating_tree_nodes reading sources... [ 85%] examples/neutral_test reading sources... [ 86%] examples/parallel reading sources... [ 87%] examples/parametric_bootstrap reading sources... [ 88%] examples/period_estimation reading sources... [ 89%] examples/phylo_by_ls reading sources... [ 90%] examples/rate_heterogeneity reading sources... [ 90%] examples/relative_rate reading sources... [ 91%] examples/scope_model_params_on_trees reading sources... [ 92%] examples/seq_features reading sources... [ 93%] examples/simple reading sources... [ 94%] examples/simulate_alignment reading sources... [ 95%] examples/testing_multi_loci reading sources... [ 96%] general reading sources... [ 97%] index reading sources... [ 98%] install reading sources... [ 99%] licenses reading sources... [100%] pycogent /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: WARNING: Unexpected section title. Notes ----- /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.to_type:11: WARNING: Field list ends without a blank line; unexpected unindent. /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: WARNING: Unexpected section title. Notes ----- /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.to_type:11: WARNING: Field list ends without a blank line; unexpected unindent. /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_unaligned(format="fasta") seqs = reader("data/SCA1-cds.fasta") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:23: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.align import progressive_align codon_aligner = progressive_align("codon") aligned = codon_aligner(seqs) aligned /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_aligner = progressive_align("codon", distance="paralinear") aligned = nt_aligner(seqs) aligned /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:57: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" codon_aligner = progressive_align("codon", guide_tree=tree) aligned = codon_aligner(seqs) aligned /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:67: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: codon_aligner = progressive_align( "codon", guide_tree=tree, indel_rate=0.001, indel_length=0.01 ) aligned = codon_aligner(seqs) aligned /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:80: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: codon_aligner = progressive_align( "CNFHKY", guide_tree=tree, param_vals=dict(omega=0.1, kappa=3) ) aligned = codon_aligner(seqs) aligned /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:91: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_unaligned(format="fasta") seqs = reader("data/SCA1-cds.fasta") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:23: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.align import progressive_align nt_aligner = progressive_align("nucleotide") aligned = nt_aligner(seqs) aligned /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_aligner = progressive_align("nucleotide", distance="TN93") aligned = nt_aligner(seqs) aligned /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:45: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = progressive_align("nucleotide", guide_tree=tree) aligned = nt_aligner(seqs) aligned /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:59: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = progressive_align("F81", guide_tree=tree) aligned = nt_aligner(seqs) aligned /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:69: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-protein.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-protein.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, translate reader = io.load_unaligned(format="fasta") to_aa = translate.translate_seqs() process = reader + to_aa seqs = process("data/SCA1-cds.fasta") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-protein.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.align import progressive_align aa_aligner = progressive_align("protein") aligned = aa_aligner(seqs) aligned /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-protein.rst:40: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa_aligner = progressive_align("protein", distance="paralinear") aligned = aa_aligner(seqs) aligned /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/align-protein.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/available-apps.rst:8: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_apps available_apps() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:24: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.io import get_data_store dstore = get_data_store("data/raw.zip", suffix="fa*", limit=5) dstore /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: m = dstore[0] m /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:41: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: m.read()[:20] # truncating /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:50: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.tail() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:57: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.filtered("*ENSG00000067704*") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:64: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for m in dstore: print(m) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:85: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = get_data_store("data/demo-locked.tinydb") dstore.describe /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:92: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.unlock(force=True) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:101: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.summary_logs /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.logs /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:113: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(dstore.logs[0].read()[:225]) # truncated for clarity /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-ancestral-states.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-ancestral-states.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo reader = io.load_aligned(format="fasta") aln = reader("data/primate_brca1.fasta") gn = evo.model("GN", tree="data/primate_brca1.tree") result = gn(aln) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-ancestral-states.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: reconstuctor = evo.ancestral_states() states_result = reconstuctor(result) states_result /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-ancestral-states.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: states_result["edge.0"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-ancestral-states.rst:39: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.tree.get_figure(contemporaneous=True).show(width=500, height=500) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = evo.model("BH", tree="data/primate_brca1.tree") result = model(aln) result /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = result.tree fig = tree.get_figure() fig.scale_bar = "top right" fig.show(width=500, height=500) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = evo.tabulate_stats() stats = tabulator(result) stats /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: stats["edge motif motif2 params"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-extract-model-stats.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-extract-model-stats.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = evo.model("GN", tree="data/primate_brca1.tree") result = model(aln) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-extract-model-stats.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = evo.tabulate_stats() tabulated = tabulator(result) tabulated /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-extract-model-stats.rst:38: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["edge params"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-extract-model-stats.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["global params"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-extract-model-stats.rst:58: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["motif params"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo, sample loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:18: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = "data/primate_brca1.tree" sm_args = dict(optimise_motif_probs=True) null = evo.model("GTR", tree=tree, sm_args=sm_args) alt = evo.model("GN", tree=tree, sm_args=sm_args) hyp = evo.hypothesis(null, alt) result = hyp(aln) type(result) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:31: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:43: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.LR, result.df, result.pvalue /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:56: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null.lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:12: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, sample reader = io.load_aligned(format="fasta", moltype="dna") select_seqs = sample.take_named_seqs("Human", "Rhesus", "Galago") process = reader + select_seqs aln = process("data/primate_brca1.fasta") aln.names /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:26: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import evo gn = evo.model("GN") gn /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) type(fitted) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:59: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lnL, fitted.nfp /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.source /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:69: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.tree, fitted.alignment /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:75: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.total_length(length_as="paralinear") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:84: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = evo.model("GN", split_codons=True) fitted = gn(aln) fitted /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:95: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted[3] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-timehet.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-timehet.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.app import io, evo tree = load_tree("data/primate_brca1.tree") fig = tree.get_figure(contemporaneous=True) fig.style_edges( "Human", tip2="Orangutan", outgroup="Galago", line=dict(color="red") ) fig.show(width=500, height=500) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-timehet.rst:32: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: time_het = evo.model( "GN", tree=tree, time_het=[dict(tip_names=["Human", "Orangutan"], outgroup_name="Galago")], ) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-timehet.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = io.load_aligned(format="fasta") aln = reader("data/primate_brca1.fasta") result = time_het(aln) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-timehet.rst:50: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_aligned(format="fasta", moltype="dna") aln = reader("data/primate_brca1.fasta") aln.names /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:22: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.app import evo tree = load_tree("data/primate_brca1.tree") gn = evo.model("GN", tree=tree) gn /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = evo.model("GN", tree="data/primate_brca1.tree") gn /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) fitted /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:51: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_neutral.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_neutral.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") omega_eq_1 = evo.natsel_neutral( "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = omega_eq_1(aln) type(result) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_neutral.rst:26: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_neutral.rst:30: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_sitehet.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_sitehet.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") sites_differ = evo.natsel_sitehet( "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = sites_differ(aln) result /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_sitehet.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_sitehet.rst:38: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = result.alt.lf.get_bin_probs() bprobs[:, :20] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_timehet.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_timehet.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io, evo loader = io.load_aligned(format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") hc_differ = evo.natsel_timehet( "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False, tip1="Human", tip2="Chimpanzee", ) result = hc_differ(aln) result /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_timehet.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_zhang.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_zhang.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from numpy import array from cogent3 import make_table from IPython.core.display import HTML header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges'] data = {'Site Class': array(['0', '1', '2a', '2b'], dtype=' 1', '0 < omega0 < 1'], dtype=' 1, motif_length=3 ) print(just_variable_aln[:9]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:553: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = aln.to_type(array_align=False) variable_codons = aln.filtered(lambda x: len(set("".join(x))) > 1, motif_length=3) print(just_variable_aln[:9]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:567: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") aln.take_seqs(["Human", "Mouse"]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:576: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs(["Human", "Mouse"], negate=True) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:585: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) def no_N_chars(s): return "N" not in s aln.take_seqs_if(no_N_chars) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:605: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs_if(no_N_chars, negate=True) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:617: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) counts = aln.counts() print(counts) counts = aln.counts(motif_length=3) print(counts) counts = aln.counts(include_ambiguity=True) print(counts) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:645: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs() print(motif_probs) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:655: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, DNA trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs(alphabet=trinuc_alphabet) for m in sorted(motif_probs, key=lambda x: motif_probs[x], reverse=True): print("%s %.3f" % (m, motif_probs[m])) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:669: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs(data=[("a", "AACAAC"), ("b", "AAGAAG")], moltype="dna") motif_probs = aln.get_motif_probs() assert motif_probs["T"] == 0.0 motif_probs = aln.get_motif_probs(pseudocount=1e-6) assert 0 < motif_probs["T"] <= 1e-6 /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:681: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("a", "AACGTAAG"), ("b", "AACGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) motif_probs = aln.get_motif_probs(alphabet=dinuc_alphabet) assert motif_probs["AA"] == 0.25 /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:691: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("my_seq", "AAAGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") my_seq = aln.get_seq("my_seq") my_seq.count("AA") "AAA".count("AA") "AAAA".count("AA") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:702: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq(moltype="dna", seq="AAAGTAAG") seq di_nucs = [seq[i : i + 2] for i in range(len(seq) - 1)] sum([nn == "AA" for nn in di_nucs]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:717: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() c1, c2 = list(col) c1, c2 list(filter(lambda x: x == "-", c1)) list(filter(lambda x: x == "-", c2)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:731: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") for column in aln[113:150].iter_positions(): ungapped = list(filter(lambda x: x == "-", column)) gap_fraction = len(ungapped) * 1.0 / len(column) print(gap_fraction) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:746: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGG-TG--"), ("seq2", "ATG-AGGTGATG"), ("seq3", "ATGAAG--GATG"), ], moltype="dna", ) seq_to_aln_map = aln.get_gapped_seq("seq1").gap_maps()[0] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:762: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq_to_aln_map[3] seq_to_aln_map[8] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:771: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_to_seq_map = aln.get_gapped_seq("seq1").gap_maps()[1] aln_to_seq_map[3] aln_to_seq_map[8] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:779: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError seq_pos = aln_to_seq_map[7] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:793: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) print(aln.omit_gap_runs(2)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:807: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) print(aln.omit_gap_pos(0.40)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:821: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) filtered_aln = aln.omit_gap_seqs(0.50) print(filtered_aln) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:836: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(filtered_aln.omit_gap_pos()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, PROTEIN print(DNA.alphabet) print(PROTEIN.alphabet) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:20: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: PROTEIN.alphabet.moltype == PROTEIN /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) print(dinuc_alphabet) trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) print(trinuc_alphabet) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:39: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = "TAGT" indices = DNA.alphabet.to_indices(seq) indices /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_indices([0, 2, 3, 0]) seq /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_ordinals_to_seq([0, 2, 3, 0]) seq /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:21: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.genbank import RichGenbankParser parser = RichGenbankParser(open("data/ST_genome_part.gb")) for accession, seq in parser: print(accession) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds = seq.get_annotations_matching("CDS") print(cds) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:39: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.annotation import Feature def add_annotation(seq, feature, spans): type_ = feature["type"] if type_ != "CDS": return name = feature.get("locus_tag", None) if name and not isinstance(name, str): name = " ".join(name) seq.add_annotation(Feature, type_, name, spans) parser = RichGenbankParser( open("data/ST_genome_part.gb"), add_annotation=add_annotation ) for accession, seq in parser: # just reading one accession,sequence break genes = seq.get_annotations_matching("CDS") print(genes) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.annotation import Feature s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) print(s1[10:15]) # this will be exon 1 print(s1[30:40]) # this will be exon 2 print(s1[45:48]) # this will be exon 3 s2 = DNA.make_seq("CGAAACGTTT", name="seq2") s3 = DNA.make_seq("CGAAACGTTT", name="seq3") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:83: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.annotation import Feature s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_annotation(Feature, "exon", "A", [(10, 15)]) exon2 = s1.add_annotation(Feature, "exon", "B", [(30, 40)]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:97: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon3 = s1.add_feature("exon", "C", [(45, 48)]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:111: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s2 = DNA.make_seq("CGAAACGTTT", name="seq2") cpgs_series = s2.add_feature("cpgsite", "cpg", [(0, 2), (5, 7)]) s3 = DNA.make_seq("CGAAACGTTT", name="seq3") cpg1 = s3.add_feature("cpgsite", "cpg", [(0, 2)]) cpg2 = s3.add_feature("cpgsite", "cpg", [(5, 7)]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:126: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_feature("exon", "A", [(10, 15)]) exon2 = s1.add_feature("exon", "B", [(30, 40)]) exon3 = s1.add_feature("exon", "C", [(45, 48)]) cds = s1.get_region_covering_all([exon1, exon2, exon3]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:143: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds.get_coordinates() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:152: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_cds = cds.get_shadow() not_cds /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:159: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:168: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln1 = make_aligned_seqs( data=[["x", "-AAACCCCCA"], ["y", "TTTT--TTTT"]], array_align=False ) seq_exon = aln1.get_seq("x").add_feature("exon", "A", [(3, 8)]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:182: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.annotation import Variable red_data = aln1.add_annotation( Variable, "redline", "align", [((0, 15), 1), ((15, 30), 2), ((30, 45), 3)] ) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:195: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_feature("exon", "A", [(10, 15)]) exon2 = s1.add_feature("exon", "B", [(30, 40)]) s1[exon1] s1[10:15] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:209: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s1[exon2] exon2.get_slice() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:217: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_feature("exon", "A", [(10, 15)]) exon2 = s1.add_feature("exon", "B", [(30, 40)]) exon3 = s1.add_feature("exon", "C", [(45, 48)]) cds = s1.get_region_covering_all([exon1, exon2, exon3]) print(s1[cds]) print(s1[exon1, exon2, exon3]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:233: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1) print(s1[exon1, exon2, exon3]) print(s1[exon2]) print(s1[exon3]) print(s1[exon1, exon3, exon2]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:244: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError s1[1:10, 9:15] s1[exon1, exon1] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:252: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1.get_region_covering_all([exon3, exon3]).get_slice()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:259: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1[exon2]) ex2_start = exon2[0:3] print(s1[ex2_start]) ex2_end = exon2[-3:] print(s1[ex2_end]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:272: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError aln1[seq_exon] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:282: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(3, 8)]) aln2.get_seq("x").copy_annotations(seq) copied = list(aln2.get_annotations_from_seq("x", "exon")) copied /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:295: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln2 = make_aligned_seqs(data=[["x", "-AAAA"], ["y", "TTTTT"]], array_align=False) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(5, 8)]) aln2.get_seq("x").copy_annotations(seq) copied = list(aln2.get_annotations_from_seq("x", "exon")) copied copied[0].get_slice() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:307: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: # new test aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(5, 8)]) aln2.get_seq("y").copy_annotations(seq) copied = list(aln2.get_annotations_from_seq("y", "exon")) copied /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:321: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) diff_len_seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCCCCCCCCCC", "x") nonmatch = diff_len_seq.add_feature("repeat", "A", [(12, 14)]) aln2.get_seq("y").copy_annotations(diff_len_seq) copied = list(aln2.get_annotations_from_seq("y", "repeat")) copied /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:337: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_exon = aln1.get_annotations_from_any_seq("exon") print(aln1[aln_exon]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:345: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError cpgsite2 = s2.get_annotations_matching("cpgsite") print(s2[cpgsite2]) cpgsite3 = s3.get_annotations_matching("cpgsite") s2[cpgsite3] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:358: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: # this test is new dont_exist = s2.get_annotations_matching("dont_exist") dont_exist s2[dont_exist] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:370: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln3 = make_aligned_seqs( data=[["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], array_align=False ) exon = aln3.get_seq("x").add_feature("exon", "ex1", [(0, 4)]) print(exon.get_slice()) aln_exons = list(aln3.get_annotations_from_seq("x", "exon")) print(aln_exons) print(aln3[aln_exons]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:388: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: unified = aln_exons[0].as_one_span() print(aln3[unified]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:398: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: plus = DNA.make_seq("CCCCCAAAAAAAAAATTTTTTTTTTAAAGG") plus_rpt = plus.add_feature("blah", "a", [(5, 15), (25, 28)]) print(plus[plus_rpt]) minus = plus.rc() print(minus) minus_rpt = minus.get_annotations_matching("blah") print(minus[minus_rpt]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:413: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.genbank import RichGenbankParser parser = RichGenbankParser(open("data/ST_genome_part.gb")) seq = [seq for accession, seq in parser][0] no_cds = seq.with_masked_annotations("CDS") print(no_cds[150:400]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:429: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]], moltype="dna", array_align=False, ) exon = aln.get_seq("x").add_feature("exon", "norwegian", [(0, 4)]) print(aln.with_masked_annotations("exon", mask_char="?")) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:443: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rc = aln.rc() print(rc) print(rc.with_masked_annotations("exon", mask_char="?")) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:452: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s = DNA.make_seq("CCCCAAAAAGGGAA", "x") exon = s.add_feature("exon", "norwegian", [(0, 4)]) rpt = s.add_feature("repeat", "norwegian", [(9, 12)]) rc = s.rc() print(s.with_masked_annotations("exon", shadow=True)) print(rc.with_masked_annotations("exon", shadow=True)) print(s.with_masked_annotations(["exon", "repeat"], shadow=True)) print(rc.with_masked_annotations(["exon", "repeat"], shadow=True)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:468: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s = DNA.make_seq("ATGACCCTGTAAAAAATGTGTTAACCC", name="a") cds1 = s.add_feature("cds", "cds1", [(0, 12)]) cds2 = s.add_feature("cds", "cds2", [(15, 24)]) all_cds = s.get_annotations_matching("cds") all_cds /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:483: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.genbank import RichGenbankParser parser = RichGenbankParser(open("data/ST_genome_part.gb")) seq = [seq for accession, seq in parser][0] all_cds = seq.get_annotations_matching("CDS") coding_seqs = seq.get_region_covering_all(all_cds) coding_seqs coding_seqs.get_slice() noncoding_seqs = coding_seqs.get_shadow() noncoding_seqs noncoding_seqs.get_slice() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:502: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) print(aln) exon = aln.get_seq("x").add_feature("exon", "1", [(3, 8)]) aln_exons = aln.get_annotations_from_seq("x", "exon") aln_exons = aln.get_annotations_from_any_seq("exon") aln_exons /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:522: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA seq = DNA.make_seq("aaaccggttt" * 10) v = seq.add_feature("exon", "exon", [(20, 35)]) v = seq.add_feature("repeat_unit", "repeat_unit", [(39, 49)]) v = seq.add_feature("repeat_unit", "rep2", [(49, 60)]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:536: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.misc import remove_files remove_files(["annotated_%d.png" % i for i in range(1, 4)], error_on_missing=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:17: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import TreeAlign /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:24: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") aln, tree = TreeAlign("HKY85", seqs, show_progress=False) aln /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:32: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = make_tree( "(((NineBande:0.013,Mouse:0.185):0.023,DogFaced:0.046):0.027,Human:0.034,HowlerMon:0.019)" ) params = {"kappa": 4.0} aln, tree = TreeAlign( "HKY85", seqs, tree=tree, param_vals=params, show_progress=False ) aln /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import TreeAlign seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") tree = make_tree( "((NineBande:0.058,Mouse:0.595):0.079,DogFaced:0.142,(HowlerMon:0.062,Human:0.103):0.079)" ) params = {"kappa": 4.0, "omega": 1.3} aln, tree = TreeAlign( "MG94HKY", seqs, tree=tree, param_vals=params, show_progress=False ) aln /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:68: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs from cogent3.evolve.models import get_model from cogent3.align.progressive import TreeAlign seqs = [ ( "hum", "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", ), ( "mus", "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", ), ("rat", "CTGAACAAGCAGCCACTTTCAAACAAGAAA"), ] unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") print(unaligned_DNA) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:88: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(unaligned_DNA.get_translation()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:94: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aligned_aa_seqs = [ ("hum", "KQIQESSENGSLAARQERQAQVNLT"), ("mus", "KQIQESGESGSLAARQERQAQVNLT"), ("rat", "LNKQ------PLS---------NKK"), ] aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA, aa_to_codon=True) aligned_DNA /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:18: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = aln.quick_tree(calc="TN93", show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = aln.quick_tree(calc="TN93", bootstrap=100, show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = dists.quick_tree(show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo import nj from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = nj.nj(dists, show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo import nj dists = {("a", "b"): 2.7, ("c", "b"): 2.33, ("c", "a"): 0.73} tree = nj.nj(dists, show_progress=False) print(tree.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:76: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.deserialise import deserialise_object from cogent3.phylo.least_squares import WLS dists = deserialise_object("data/dists_for_phylo.json") ls = WLS(dists) stat, tree = ls.trex(a=5, k=5, show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:92: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.phylo.maximum_likelihood import ML from cogent3.evolve.models import F81 aln = load_aligned_seqs("data/primate_brca1.fasta") ml = ML(F81(), aln) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:16: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_distances available_distances() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:38: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, get_distance_calculator aln = load_aligned_seqs("data/primate_brca1.fasta") dist_calc = get_distance_calculator("tn93", alignment=aln) dist_calc /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.run(show_progress=False) dists = dist_calc.get_pairwise_distances() dists /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.stderr /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:65: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, get_model from cogent3.evolve import distance aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") d = distance.EstimateDistances(aln, submodel=get_model("F81")) d.run(show_progress=False) dists = d.get_pairwise_distances() dists /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:18: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model hky = get_model("HKY85") print(hky) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:44: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("GTR", with_rate=True, distribution="gamma") print(sub_mod) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:56: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("CNFGTR", with_rate=True, distribution="gamma") print(sub_mod) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:68: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("JTT92", with_rate=True, distribution="gamma") print(sub_mod) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:80: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:94: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree, make_aligned_seqs from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) aln = make_aligned_seqs( [("a", "ACGT"), ("b", "AC-T"), ("c", "ACGT"), ("d", "AC-T")] ) lf.set_alignment(aln) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:112: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") print(tree.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:120: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule( "omega", tip_names=["Human", "Orangutan"], outgroup_name="Galago", clade=True, init=0.5, ) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:134: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:145: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", is_constant=True) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:160: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:175: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1, lower=1e-9, upper=20.0) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:190: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_param_rule("length", upper=1.0) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:207: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, digits=2) lf.set_param_rule("bprobs", is_constant=True) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:222: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, sites_independent=False, digits=2) lf.set_param_rule("bprobs", is_constant=True) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:239: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:253: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, max_restarts=5, show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:259: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=False, global_tolerance=1.0, show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:265: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False, max_restarts=5, tolerance=1e-8) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:276: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) try: lf.optimise( show_progress=False, limit_action="raise", max_evaluations=10, return_calculator=True, ) except ArithmeticError as err: print(err) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:303: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model sm = get_model("GTR") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree) aln = load_aligned_seqs("data/primate_brca1.fasta") lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:321: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lnL = lf.lnL lnL /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:326: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: nfp = lf.nfp nfp /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:338: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:344: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic(second_order=True) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:353: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_bic() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:367: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: a_g = lf.get_param_value("A/G") a_g /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:372: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: human = lf.get_param_value("length", "Human") human /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:380: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mprobs = lf.get_motif_probs() mprobs /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:388: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tables = lf.get_statistics(with_motif_probs=True, with_titles=True) tables[0] # just displaying the first /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:398: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) null_lnL = lf.lnL null_nfp = lf.nfp lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:423: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) lf.set_name("Alt Hypothesis") lf.optimise(local=True, show_progress=False) alt_lnL = lf.lnL alt_nfp = lf.nfp lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:434: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats import chisqprob LR = 2 * (alt_lnL - null_lnL) # the likelihood ratio statistic df = alt_nfp - null_nfp # the test degrees of freedom p = chisqprob(LR, df) print(f"LR={LR:.4f} ; df={df}; p={df:.4f}") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:450: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) sim_aln = lf.simulate_alignment() sim_aln[:60] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:478: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("HKY85") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) kappa_lo, kappa_mle, kappa_hi = lf.get_param_interval("kappa") print(f"lo={kappa_lo:.2f} ; mle={kappa_mle:.2f} ; hi={kappa_hi:.2f}") human_lo, human_mle, human_hi = lf.get_param_interval("length", "Human") print(f"lo={human_lo:.2f} ; mle={human_mle:.2f} ; hi={human_hi:.2f}") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:501: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model aln = make_aligned_seqs(data=dict(a="ACGG", b="ATAG", c="ATGG")) tree = make_tree(tip_names=aln.names) sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) json = lf.to_json() json[:60] # just truncating the displayed string /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:516: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.deserialise import deserialise_object newlf = deserialise_object(json) newlf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:528: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, load_aligned_seqs from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:542: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestors = lf.likely_ancestral_seqs() ancestors[:60] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:549: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestral_probs = lf.reconstruct_ancestral_seqs() ancestral_probs["root"][:5] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:4: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:16: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq, get_code standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") translations = standard_code.sixframes(seq) print(translations) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq, get_code standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") stops_frame1 = standard_code.get_stop_indices(seq, start=0) stops_frame1 stop_index = stops_frame1[0] seq[stop_index : stop_index + 3] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq, get_code standard_code = get_code(1) standard_code["TTT"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:51: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: standard_code["A"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:58: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["TTT"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:68: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["A"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:78: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: targets = ["A", "C"] codons = [standard_code[aa] for aa in targets] codons flat_list = sum(codons, []) flat_list /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:89: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGTT", moltype="dna") sorted(my_seq.codon_alphabet()) len(my_seq.codon_alphabet()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:102: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna") codons = my_seq.get_in_motif_size(3) print(codons) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:115: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AlphabetError pep = my_seq.get_translation() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:123: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna") seq = my_seq.trim_stop_codon() pep = seq.get_translation() print(pep.to_fasta()) print(type(pep)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:136: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("CAAATGTATTAA", name="my_gene", moltype="dna") pep = my_seq[:-3].get_translation() print(pep.to_fasta()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:16: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna") type(aln) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.info.source /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:38: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/long_testseqs.fasta", moltype="dna") type(seqs) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:50: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna", format="fasta") aln /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:62: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs protein_seqs = [">seq1", "DEKQL-RG", ">seq2", "DDK--SRG"] proteins_loaded = make_aligned_seqs(protein_seqs) proteins_loaded.moltype print(proteins_loaded) proteins_loaded = make_aligned_seqs(protein_seqs, moltype="protein") print(proteins_loaded) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:81: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"} seqs_loaded = make_aligned_seqs(seqs) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:91: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = [">seq1", "AATCG-A", ">seq2", "AATCGGA"] seqs_loaded = make_aligned_seqs(seqs) print(seqs_loaded) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:104: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs DNA_seqs = [ ">sample1 Mus musculus", "AACCTGC--C", ">sample2 Gallus gallus", "AAC-TGCAAC", ] loaded_seqs = make_aligned_seqs( DNA_seqs, moltype="dna", label_to_name=lambda x: x.split()[0] ) loaded_seqs /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:124: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs seqs = {"seq1": "AATCA", "seq2": "AATCGGA"} seqs = make_unaligned_seqs(data=seqs, moltype="dna") seqs /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:144: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import MinimalFastaParser f = open("data/long_testseqs.fasta") seqs = [(name, seq) for name, seq in MinimalFastaParser(f)] seqs /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:157: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import LabelParser def latin_to_common(latin): return {"Homo sapiens": "human", "Pan troglodtyes": "chimp"}[latin] label_parser = LabelParser( "%(species)s", [[1, "species", latin_to_common]], split_with=":" ) for label in ">abcd:Homo sapiens:misc", ">abcd:Pan troglodtyes:misc": label = label_parser(label) print(label, type(label)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:173: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import MinimalFastaParser, LabelParser fasta_data = [ ">gi|10047090|ref|NP_055147.1| small muscle protein, X-linked [Homo sapiens]", "MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGAKKLPGPAVNL", "SEIQNIKSELKYVPKAEQ", ">gi|10047092|ref|NP_037391.1| neuronal protein [Homo sapiens]", "MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLY", "PPGQEPIPKISESKMAFKQMEQISQFLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTKD", ] label_to_name = LabelParser( "%(ref)s", [[1, "gi", str], [3, "ref", str], [4, "description", str]], split_with="|", ) for name, seq in MinimalFastaParser(fasta_data, label_to_name=label_to_name): print(name) print(name.info.gi) print(name.info.description) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:44: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:70: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:82: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:94: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:117: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:132: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:141: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:150: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:164: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:175: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:185: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:190: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:199: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:213: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:225: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:236: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:268: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:283: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:17: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_moltypes available_moltypes() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_moltype dna = get_moltype("dna") dna /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.ambiguities /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.degenerates /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:60: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.complement("AGG") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:69: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = dna.make_seq("AGGCTT", name="seq1") seq /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:77: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rna = get_moltype("rna") rna.is_valid("ACGUACGUACGUACGU") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:87: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core import moltype as mt DNAgapped = mt.MolType( seq_constructor=mt.DnaSequence, motifset=mt.IUPAC_DNA_chars, ambiguities=mt.IUPAC_DNA_ambiguities, complements=mt.IUPAC_DNA_ambiguities_complements, pairs=mt.DnaStandardPairs, gaps=".", ) seq = DNAgapped.make_seq("ACG.") seq /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:104: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.sequence import DnaSequence DnaSequence.moltype = DNA /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/protein_sequences.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/protein_sequences.rst:14: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import PROTEIN p = PROTEIN.make_seq("THISISAPRQTEIN", "myProtein") type(p) str(p) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/protein_sequences.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.genetic_code import DEFAULT as standard_code standard_code.translate("TTTGCAAAC") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/protein_sequences.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:14: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:24: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.write("data/temp.tree") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") names = tr.get_node_names() names[:4] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: names[4:] names_nodes = tr.get_nodes_dict() names_nodes["Human"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_node_matching_name("Mouse") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tr.name /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: hu.name /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:70: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] type(hu) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:79: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(tr) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:88: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() for n in nodes.items(): print(n) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:99: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tr.iter_tips(): print(n) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:106: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for n in tr.iter_nontips(): print(n.get_newick()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:117: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") edges = tr.get_connecting_edges("edge.1", "Human") for edge in edges: print(edge.name) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:129: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] hu.distance(mu) hu.is_tip() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:143: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] lca = hu.last_common_ancestor(mu) lca /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:154: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(lca) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:161: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") for a in hu.ancestors(): print(a.name) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:173: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") node = tr.get_node_matching_name("edge.1") children = list(node.iter_tips()) + list(node.iter_nontips()) for child in children: print(child.name) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:186: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") dists = tr.get_distances() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:195: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: human_dists = [names for names in dists if "Human" in names] for dist in human_dists: print(dist, dists[dist]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:204: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.max_tip_tip_distance() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:214: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tips = hu.tips_within_distance(0.2) for t in tips: print(t) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:230: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.rooted_at("edge.0").ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:240: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.root_at_midpoint().ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:247: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:254: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:261: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.rooted_with_tip("Mouse").ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:271: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.get_newick() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:278: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_newick(with_distances=True) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:285: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") xml = tr.get_xml() for line in xml.splitlines(): print(line) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:299: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:309: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.preorder(): print(t.get_newick()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:320: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.postorder(): print(t.get_newick()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:334: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for tip in tr.iter_nontips(): tip_names = tip.get_tip_names() print(tip_names) sub_tree = tr.get_sub_tree(tip_names) print(sub_tree.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:348: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.misc import remove_files remove_files(["data/temp.tree", "data/temp.pdf"], error_on_missing=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:364: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree simple_tree_string = "(B:0.2,(D:0.4)E:0.5)F;" simple_tree = make_tree(simple_tree_string) print(simple_tree.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:372: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.prune() print(simple_tree.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:377: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:384: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = load_tree("data/test.tree") print(tr1.get_newick()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:391: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr2 = tr1.unrooted_deepcopy() print(tr2.get_newick()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:401: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tree_string = "(B:0.2,H:0.2,(C:0.3,D:0.4,E:0.1)F:0.5)G;" tr = make_tree(tree_string) print(tr.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:409: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.bifurcating().ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:422: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:429: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.balanced().ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:438: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = make_tree("(B:0.2,(C:0.2,D:0.2)F:0.2)G;") tr2 = make_tree("((C:0.1,D:0.1)F:0.1,B:0.1)G;") tr1.same_topology(tr2) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:452: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:459: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.set_tip_distances() for t in tr.preorder(): print(t.name, t.TipDistance) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:468: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:475: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.scale_branch_lengths() print(tr) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:485: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = make_tree("(B:3,(C:2,D:4)F:5)G;") d, tips = tr.tip_to_tip_distances() for i, t in enumerate(tips): print(t.name, d[i]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:505: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = make_tree("(B:2,(C:3,D:4)F:5)G;") tr2 = make_tree("(C:2,(B:3,D:4)F:5)G;") tr1.compare_by_tip_distances(tr2) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory cookbook/loading_tabular.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory cookbook/loading_tabular.rst:11: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table cookbook/loading_tabular.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table cookbook/loading_tabular.rst:44: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] cookbook/loading_tabular.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] cookbook/loading_tabular.rst:70: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table cookbook/loading_tabular.rst:82: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table cookbook/loading_tabular.rst:94: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table cookbook/loading_tabular.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table cookbook/loading_tabular.rst:117: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table cookbook/loading_tabular.rst:132: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) cookbook/loading_tabular.rst:141: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] cookbook/loading_tabular.rst:150: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table cookbook/loading_tabular.rst:164: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table cookbook/loading_tabular.rst:175: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table cookbook/loading_tabular.rst:185: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] cookbook/loading_tabular.rst:190: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] cookbook/loading_tabular.rst:199: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table cookbook/loading_tabular.rst:213: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table cookbook/loading_tabular.rst:225: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table cookbook/loading_tabular.rst:236: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table cookbook/loading_tabular.rst:268: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table cookbook/loading_tabular.rst:283: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:21: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data, title="Sample title", legend="a legend") table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:45: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table.title = "My title" table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:57: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") for row in table: print(row) break /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:68: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for row in table: print(row["Locus"]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:78: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3, 5], b=["a", "c", "d"]) table = make_table(data=data) table.shape[0] == 3 /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:91: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.shape[1] == 2 /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:100: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.columns /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Region"] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:113: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for name in table.columns: print(name) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:121: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:128: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table[:2, "Region":] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:135: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table[:2, :1] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:145: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.format_column("Ratio", "%.1e") table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:158: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", digits=1, space=2) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:165: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.space = " " table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:175: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table h = ["name", "A/C", "A/G", "A/T", "C/A"] rows = [["tardigrade", 0.0425, 0.1424, 0.0226, 0.0391]] wrap_table = make_table(header=h, data=rows, max_width=30) wrap_table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:184: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: wrap_table = make_table(header=h, data=rows, max_width=30, index_name="name") wrap_table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:192: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data=dict(a=list(range(10)), b=list(range(10)))) table.head() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:199: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.head(2) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:208: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:214: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail(1) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:221: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(random=3) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:229: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(head=2, tail=3) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:241: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.header) table = table.with_new_header("Ratio", "Stat") print(table.header) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:251: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:258: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:269: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table = table.with_new_column( "LargeCon", lambda r_v: r_v[0] == "Con" and r_v[1] > 10.0, columns=["Region", "Ratio"], ) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:282: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.array /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:292: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") locus = table.tolist("Locus") locus /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:300: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Locus"].tolist() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:309: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") rows = table.tolist(["Region", "Locus"]) rows /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:322: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.to_dict() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:332: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.columns.to_dict() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:340: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") df = table.to_dataframe() df /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:348: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: df = table.to_dataframe(categories="Region") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:357: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}, index_name="") table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:362: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: contingency = table.to_categorical(["Ts", "Tv"]) contingency /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:367: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: g_test = contingency.G_independence() g_test /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:374: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}) contingency = table.to_categorical(["Ts", "Tv"], index_name="") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:386: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1 = load_table("data/stats.tsv") table2 = load_table("data/stats.tsv") table = table1.appended(None, table2) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:395: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1.title = "Data1" table2.title = "Data2" table = table1.appended("Data#", table2, title="") table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:407: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.summed("Ratio") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:414: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Ratio"].sum() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:423: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table all_numeric = make_table( header=["A", "B", "C"], data=[range(3), range(3, 6), range(6, 9), range(9, 12)] ) all_numeric /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:434: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:440: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed(col_sum=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:449: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed = make_table( header=["A", "B", "C"], data=[["*", 1, 2], [3, "*", 5], [6, 7, "*"]] ) mixed /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:458: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(strict=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:464: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(col_sum=False, strict=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:473: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") sub_table = table.filtered(lambda x: x < 10.0, columns="Ratio") sub_table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:481: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0") sub_table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:488: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0 and Region == 'NonCon'") sub_table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:498: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: big_numeric = all_numeric.filtered_by_column(lambda x: sum(x) > 20) big_numeric /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:506: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.sorted(columns="Ratio") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:514: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns="Ratio", reverse="Ratio") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:521: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns=["Region", "Ratio"], reverse="Ratio") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:528: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.tolist("Region") raw /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:537: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.tolist(["Locus", "Region"]) raw /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:546: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.distinct_values("Region") == set(["NonCon", "Con"]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:554: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.count("Region == 'NonCon' and Ratio > 1") == 1 /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:564: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( data=dict(A=["a", "b", "b", "b", "a"], B=["c", "c", "c", "c", "d"]) ) unique = table.count_unique("A") type(unique) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:574: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:580: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique = table.count_unique(["A", "B"]) unique /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:585: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: r = unique.to_table() r /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:595: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rows = [ ["NP_004893", True], ["NP_005079", True], ["NP_005500", False], ["NP_055852", False], ] region_type = make_table(header=["Locus", "LargeCon"], data=rows) stats_table = load_table("data/stats.tsv") new = stats_table.joined(region_type, columns_self="Locus") new /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:615: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["#OTU ID", "14SK041", "14SK802"] rows = [ [-2920, "332", 294], [-1606, "302", 229], [-393, 141, 125], [-2109, 138, 120], ] table = make_table(header=header, rows=rows) table /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:631: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tp = table.transposed(new_column_name="sample", select_as_header="#OTU ID") tp /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:641: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="md") print(table) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:653: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="tex") print(table) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:665: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_markdown(justify="ccr")) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:673: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_latex(justify="ccr", label="tab:table1")) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:683: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst(csv_table=True)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:693: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:705: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_string(format="latex")) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:715: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: rows = [ ["1", 100, 101, 1.123], ["1", 101, 102, 1.123], ["1", 102, 103, 1.123], ["1", 103, 104, 1.123], ["1", 104, 105, 1.123], ["1", 105, 106, 1.123], ["1", 106, 107, 1.123], ["1", 107, 108, 1.123], ["1", 108, 109, 1], ["1", 109, 110, 1], ["1", 110, 111, 1], ["1", 111, 112, 1], ["1", 112, 113, 1], ["1", 113, 114, 1], ["1", 114, 115, 1], ["1", 115, 116, 1], ["1", 116, 117, 1], ["1", 117, 118, 1], ["1", 118, 119, 2], ["1", 119, 120, 2], ["1", 120, 121, 2], ["1", 150, 151, 2], ["1", 151, 152, 2], ["1", 152, 153, 2], ["1", 153, 154, 2], ["1", 154, 155, 2], ["1", 155, 156, 2], ["1", 156, 157, 2], ["1", 157, 158, 2], ["1", 158, 159, 2], ["1", 159, 160, 2], ["1", 160, 161, 2], ] bgraph = make_table(header=["chrom", "start", "end", "value"], rows=rows) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:754: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: bgraph.head() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:760: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print( bgraph.to_string( format="bedgraph", name="test track", description="test of bedgraph", color=(255, 0, 0), digits=0, ) ) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:775: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") straight_html = table.to_html() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:787: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.format.table import known_formats known_formats /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:796: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.write("stats_tab.tex", justify="ccr", label="tab:table1") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:805: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.write("stats_tab.txt", sep="\t") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:812: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib for name in ("stats_tab.txt", "stats_tab.tex"): p = pathlib.Path(name) if p.exists(): p.unlink() cookbook/union_dict.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.a cookbook/union_dict.rst:20: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data["a"] cookbook/union_dict.rst:24: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.d cookbook/union_dict.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.b |= {"d": 25} data.b cookbook/union_dict.rst:43: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.union({"d": [25]}) cookbook/union_dict.rst:47: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b {"c": 24, "d": [25]} cookbook/union_dict.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data["k"] cookbook/union_dict.rst:65: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AttributeError data.k /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:16: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy def DiffOmega(omega): def omega_from_S(S): omega_est = S / (1 - numpy.e ** (-1 * S)) return abs(omega - omega_est) ** 2 return omega_from_S omega = 0.1 f = DiffOmega(omega) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:32: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.optimisers import minimise, maximise S = minimise( f, # the function xinit=1.0, # the initial value bounds=(-100, 100), # [lower,upper] bounds for the parameter local=True, # just local optimisation, not Simulated Annealing show_progress=False, ) assert 0.0 <= f(S) < 1e-6 print("S=%.4f" % S) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:58: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3.util.misc import iterable my_var = 10 for i in my_var: print("will not work") for i in iterable(my_var): print(i) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:75: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import curry def foo(x, y): """Some function""" return x + y bar = curry(foo, 5) print(bar.__doc__) bar(10) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:92: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_iterable can_iter = [1, 2, 3, 4] cannot_iter = 1.234 is_iterable(can_iter) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:100: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_iterable(cannot_iter) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:109: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_char class foo: pass is_char("a") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:118: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char("ab") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:122: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char(foo()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:131: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import recursive_flatten l = [[[[1, 2], "abcde"], [5, 6]], [7, 8], [9, 10]] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:137: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: recursive_flatten(l) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:146: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import not_list_tuple not_list_tuple(1) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:152: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple([1]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:156: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple("ab") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:165: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import add_lowercase d = {"A": 5, "B": 6, "C": 7, "foo": 8, 42: "life"} add_lowercase(d) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:177: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import DistanceFromMatrix from numpy import array m = array([[1, 2, 3], [4, 5, 6], [7, 8, 9]]) f = DistanceFromMatrix(m) f(0, 0) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:186: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(1, 2) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:195: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ClassChecker class not_okay(object): pass no = not_okay() class okay(object): pass o = okay() class my_dict(dict): pass md = my_dict() cc = ClassChecker(str, okay, dict) o in cc /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:216: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: no in cc /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:220: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: 5 in cc /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:224: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: {"a": 5} in cc /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:228: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: "asasas" in cc /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:232: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: md in cc /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:241: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import Delegator class ListAndString(list, Delegator): def __init__(self, items, string): Delegator.__init__(self, string) for i in items: self.append(i) ls = ListAndString([1, 2, 3], "ab_cd") len(ls) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:254: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls[0] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:258: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.upper() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:262: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.split("_") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:271: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import FunctionWrapper f = FunctionWrapper(str) f /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:278: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(123) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:289: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ConstrainedDict d = ConstrainedDict({"a": 1, "b": 2, "c": 3}, constraint="abc") d /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:296: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ConstraintError d["d"] = 5 /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/what_codes.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/what_codes.rst:10: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_codes available_codes() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/what_codes.rst:20: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs nt_seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") nt_seqs[:21] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/what_codes.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa_seqs = nt_seqs.get_translation(gc=1, incomplete_ok=True) aa_seqs[:20] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/cookbook/what_codes.rst:39: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(4) gc /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/align_codons_to_protein.rst:8: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs, make_aligned_seqs /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/align_codons_to_protein.rst:14: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = { "hum": "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", "mus": "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", "rat": "CTGAACAAGCAGCCACTTTCAAACAAGAAA", } unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") print(unaligned_DNA.to_fasta()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/align_codons_to_protein.rst:26: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_aa = unaligned_DNA.get_translation() print(unaligned_aa.to_fasta()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/align_codons_to_protein.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_aa_seqs = { "hum": "KQIQESSENGSLAARQERQAQVNLT", "mus": "KQIQESGESGSLAARQERQAQVNLT", "rat": "LNKQ------PLS---------NKK", } aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA) aligned_DNA /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:15: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.cluster.UPGMA import upgma /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:23: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/test.paml") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster = upgma(d.get_pairwise_distances()) print(mycluster.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster.write("test_upgma.tree") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_upgma.tree") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.phylo import nj /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:21: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=get_model("HKY85")) d.run(show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:40: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree = nj.nj(d.get_pairwise_distances(), show_progress=False) print(mytree.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:47: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree.write("test_nj.tree") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_nj.tree") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:15: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:22: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) d.get_pairwise_distances() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:44: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: d.write("dists_for_phylo.phylip", format="phylip") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:61: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os for file_name in "dists_for_phylo.phylip", "dists_for_phylo.pickle": os.remove(file_name) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:42: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: tf = get_model("GY94") nf = get_model("MG94GTR") cnf = get_model("CNFGTR") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = load_tree("data/primate_brca1.tree") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:64: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_param_rule("omega", is_constant=True, value=1.0) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:73: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: optimiser_args = dict( local=True, max_restarts=5, tolerance=1e-8, show_progress=False ) lf.set_alignment(aln) lf.optimise(**optimiser_args) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:92: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: neutral_lnL = lf.get_log_likelihood() neutral_nfp = lf.get_num_free_params() lf.set_param_rule("omega", is_constant=False) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:104: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats import chisqprob LR = 2 * (non_neutral_lnL - neutral_lnL) df = non_neutral_nfp - neutral_nfp print(chisqprob(LR, df)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:114: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Chimpanzee", "Human"], outgroup_name="Galago", clade=True ) lf.optimise(**optimiser_args) lf chimp_human_clade_lnL = lf.get_log_likelihood() chimp_human_clade_nfp = lf.get_num_free_params() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:124: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (chimp_human_clade_lnL - non_neutral_lnL) df = chimp_human_clade_nfp - non_neutral_nfp print(chisqprob(LR, df)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:137: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:149: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: annot_tree = lf.get_annotated_tree() omega_mle = lf.get_param_value("omega") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:156: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf = cnf.make_likelihood_function( annot_tree, bins=["neutral", "adaptive"], digits=2, space=3 ) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:164: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:170: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("omega", bin="neutral", upper=1, init=omega_mle) rate_lf.set_param_rule( "omega", bin="adaptive", lower=1 + epsilon, upper=100, init=1 + 2 * epsilon ) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:179: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("bprobs", init=[1 - epsilon, epsilon]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:185: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_alignment(aln) rate_lf.optimise(**optimiser_args) rate_lnL = rate_lf.get_log_likelihood() rate_nfp = rate_lf.get_num_free_params() LR = 2 * (rate_lnL - non_neutral_lnL) df = rate_nfp - non_neutral_nfp rate_lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:195: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(chisqprob(LR, df)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:201: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: pp = rate_lf.get_bin_probs() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:212: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from numpy import array from cogent3 import make_table from IPython.core.display import HTML header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges'] data = {'Site Class': array(['0', '1', '2a', '2b'], dtype=' 1', '0 < omega0 < 1'], dtype=' 1.8: tips_to_delete.append(n) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:121: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tips_to_delete: n.parent.remove(n) complex_tree.prune() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:129: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(complex_tree.ascii_art(show_internal=False)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from cogent3.maths import stats /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:21: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree("data/test.tree") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("MG94GTR") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=2) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:40: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(al) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(global_tolerance=1.0, show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:58: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:65: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:71: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:77: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:83: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: at = lf.get_annotated_tree() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:89: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = stats.chisqprob(LR, df) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:97: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(f"Likelihood ratio statistic = {LR}") print(f"degrees-of-freedom = {df}") print(f"probability = {P}") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:17: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve import bootstrap from cogent3.evolve.models import HKY85 from cogent3.maths import stats /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_alt_function(): t = load_tree("data/test.tree") sm = HKY85() return sm.make_likelihood_function(t) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:37: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_null_function(): lf = create_alt_function() # set the local clock for humans & howler monkey lf.set_local_clock("Human", "HowlerMon") return lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:47: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP = bootstrap.EstimateProbability( create_null_function(), create_alt_function(), aln ) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:61: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.set_num_replicates(5) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:67: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.run(show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:73: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: p = estimateP.get_estimated_prob() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:79: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("%.2f, %.2f" % estimateP.get_observed_lnL()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:26: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import numpy numpy.random.seed(11) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy t = numpy.arange(0, 10, 0.1) n = numpy.random.randn(len(t)) nse = numpy.convolve(n, numpy.exp(-t / 0.05)) * 0.1 nse = nse[: len(t)] sig = numpy.sin(2 * numpy.pi * t) + nse /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import dft pwr, period = dft(sig) print(period) print(pwr) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:58: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: pwr = abs(pwr) max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:69: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr pwr, period = auto_corr(sig) print(period) print(pwr) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:79: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:89: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s = ( "ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG" "GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT" "AATTTTTAACCGCGGAATTGCGTC" ) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:99: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"]) symbols = seq_to_symbols(s) len(symbols) == len(s) symbols /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:110: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import ipdft powers, periods = ipdft(symbols) powers /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:117: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:123: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr, hybrid powers, periods = auto_corr(symbols) powers /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:130: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:134: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = hybrid(symbols) powers /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:139: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:151: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel pwr = goertzel(sig, 10) print(pwr) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:165: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = auto_corr(symbols) llim = 2 period5 = 5 - llim periods[period5] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:172: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers[period5] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:178: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel period = 4 power = goertzel(symbols, period) ipdft_powers, periods = ipdft(symbols) ipdft_power = abs(ipdft_powers[period - llim]) round(power, 6) == round(ipdft_power, 6) power /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:191: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: power = hybrid(symbols, period=period) power /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:204: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Goertzel goertzel_calc = Goertzel(len(sig), period=10) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:212: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap obs_stat, p = blockwise_bootstrap( sig, calc=goertzel_calc, block_size=10, num_reps=1000 ) print(obs_stat) print(p) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:230: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Hybrid hybrid_calculator = Hybrid(len(s), period=4) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:240: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"], length=len(s)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:248: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap stat, p = blockwise_bootstrap( s, calc=hybrid_calculator, block_size=10, num_reps=1000, seq_to_symbols=seq_to_symbols, ) print(stat) p < 0.1 /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:15: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pickle from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.evolve.models import HKY85 from cogent3.evolve.fast_distance import DistanceMatrix al = load_aligned_seqs("data/long_testseqs.fasta") d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:31: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle from cogent3.phylo import least_squares /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:38: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: with open("dists_for_phylo.pickle", "rb") as f: dists = pickle.load(f) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:47: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls = least_squares.WLS(dists) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls_distance_matrix = least_squares.WLS(DistanceMatrix(dists)) ls_pairwise_matrix = least_squares.WLS(dists.to_dict()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:65: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: score, tree = ls.trex(a=5, k=1, show_progress=False) assert score < 1e-4 /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:77: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: trees = ls.trex(a=5, k=5, return_all=True, show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:83: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(len(trees)) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:89: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls_stats = [tree[0] for tree in trees] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:101: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: t1 = trees[0][1].balanced() t2 = trees[1][1].balanced() print(t1.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(t2.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:118: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree query_tree = make_tree( "((Human:.2,DogFaced:.2):.3,(NineBande:.1, Mouse:.5):.2,HowlerMon:.1)" ) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:128: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.evaluate_tree(query_tree) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:134: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls, t = ls.evaluate_topology(query_tree) assert "%.4f" % wls == "0.0084" /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:146: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("dists_for_phylo.pickle") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/rate_heterogeneity.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/rate_heterogeneity.rst:15: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.substitution_model import TimeReversibleNucleotide from cogent3 import load_tree /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/rate_heterogeneity.rst:22: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide(equal_motif_probs=True) tree = load_tree("data/test.tree") lf = model.make_likelihood_function(tree) lf.set_param_rule("length", value=0.6, is_constant=True) aln1 = lf.simulate_alignment(sequence_length=10000) lf.set_param_rule("length", value=0.2, is_constant=True) aln2 = lf.simulate_alignment(sequence_length=10000) aln3 = aln1 + aln2 /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/rate_heterogeneity.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="free" ) lf = model.make_likelihood_function(tree, bins=2, digits=2, space=3) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/rate_heterogeneity.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = [t for t in lf.get_statistics() if "bin" in t.title][0] bprobs /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/rate_heterogeneity.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="gamma" ) lf = model.make_likelihood_function(tree, bins=4) lf.set_param_rule("bprobs", is_constant=True) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from cogent3.maths import stats /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:21: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree(filename="data/test.tree") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("HKY85") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=3) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:40: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_local_clock("Human", "HowlerMon") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(aln) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:58: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("clock") lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:65: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:72: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:78: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:84: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("non clock") lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:91: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = stats.chisqprob(LR, df) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:99: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("Likelihood ratio statistic = ", LR) print("degrees-of-freedom = ", df) print("probability = ", P) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:17: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import MG94HKY aln = load_aligned_seqs("data/long_testseqs.fasta") tree = load_tree("data/test.tree") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = MG94HKY() lf = sm.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tree.ascii_art()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["DogFaced", "Mouse"], outgroup_name="Human", init=2.0, clade=True, ) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:73: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", init=1.0) lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=False, ) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:91: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:96: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=True, ) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:160: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:165: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, value=1.0, is_constant=True, ) lf.optimise(local=True, show_progress=False) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:180: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_constant=False, ) lf.optimise(local=True, show_progress=False) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:194: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_independent=True, ) lf.optimise(local=True, show_progress=False) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:208: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) lf.optimise(local=True, show_progress=False) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:14: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s = DNA.make_seq("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", name="Orig") exon1 = s.add_feature("exon", "exon1", [(10, 15)]) exon2 = s.add_feature("exon", "exon2", [(30, 40)]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:26: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.annotation import Feature s2 = DNA.make_seq("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", name="Orig2") exon3 = s2.add_annotation(Feature, "exon", "exon1", [(35, 40)]) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:41: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: exons = s.get_annotations_matching("exon") print(exons) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s.get_region_covering_all(exons)) s.get_region_covering_all(exons).get_slice() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s.get_region_covering_all(exons).get_shadow().get_slice()) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: exon1[0:3].get_slice() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/simple.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/simple.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model from cogent3 import load_aligned_seqs, make_tree model = get_model("HKY85") aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") tree = make_tree(tip_names=aln.names) lf = model.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(show_progress=False) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/simulate_alignment.rst:8: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: import sys from cogent3 import make_tree from cogent3.evolve.models import get_model /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/simulate_alignment.rst:16: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: t = make_tree("(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);") /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/simulate_alignment.rst:22: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("F81") lf = sm.make_likelihood_function(t) lf.set_constant_lengths() lf.set_motif_probs(dict(A=0.1, C=0.2, G=0.3, T=0.4)) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/simulate_alignment.rst:32: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: simulated = lf.simulate_alignment(sequence_length=1000) simulated /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:1: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:13: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_tree, make_table from cogent3.evolve.models import HKY85 from cogent3.recalculation.scope import EACH, ALL from cogent3.maths.stats import chisqprob aln = load_aligned_seqs("data/long_testseqs.fasta") half = len(aln) // 2 aln1 = aln[:half] aln2 = aln[half:] /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: loci_names = ["1st-half", "2nd-half"] loci = [aln1, aln2] tree = make_tree(tip_names=aln.names) mod = HKY85() /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = mod.make_likelihood_function(tree, loci=loci_names, digits=2, space=3) lf.set_param_rule("length", is_independent=False) lf.set_param_rule("kappa", loci=ALL) lf.set_alignment(loci) lf.optimise(show_progress=False) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:45: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_lnL = lf.lnL all_nfp = lf.nfp lf.set_param_rule("kappa", loci=EACH) lf.optimise(show_progress=False) lf /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: each_lnL = lf.lnL each_nfp = lf.nfp LR = 2 * (each_lnL - all_lnL) df = each_nfp - all_nfp /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:62: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: make_table( header=["LR", "df", "p"], rows=[[LR, df, chisqprob(LR, df)]], digits=2, space=3, ) /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/index.rst:8: WARNING: Unknown directive type "dropdown". .. dropdown:: Click to see an animation showing testing a hypothesis involving a non-stationary nucleotide process. .. raw:: html /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/index.rst:16: WARNING: Unknown directive type "dropdown". .. dropdown:: Click to see an animation showing defining and using sequence annotations. .. raw:: html /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/index.rst:22: WARNING: Unknown directive type "panels". .. panels:: :header: bg-primary :footer: text-right --- ``cogent3`` apps ^^^^^^^^^^^^^^^^ ``cogent3`` comes with pre-defined "apps" that simplify otherwise complex tasks. They provide capabilities that can be used by themselves, or added together to define a pipeline. They also simplify parallel execution of pipelines. +++++++++++ .. link-button:: app/index :type: ref :text: … :classes: stretched-link --- Cookbook ^^^^^^^^ The cookbook presents short code recipes targeted at specific problems. +++++++++++ .. link-button:: cookbook/index :type: ref :text: … :classes: stretched-link --- Tutorials ^^^^^^^^^ The tutorials present code for solving more extensive problems. +++++++++++ .. link-button:: examples/index :type: ref :text: … :classes: stretched-link --- API ^^^ The API for major ``cogent3`` objects +++++++++++ .. link-button:: api/index :type: ref :text: … :classes: stretched-link looking for now-outdated files... none found pickling environment... done checking consistency... /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/data_file_links.rst: WARNING: document isn't included in any toctree /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/general.rst: WARNING: document isn't included in any toctree /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/install.rst: WARNING: document isn't included in any toctree /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/licenses.rst: WARNING: document isn't included in any toctree /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc/pycogent.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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[ 48%] data/refseqs_protein.fasta copying downloadable files... [ 52%] data/inseqs.fasta copying downloadable files... [ 56%] data/inseqs_protein.fasta copying downloadable files... [ 60%] data/SCA1-cds.fasta copying downloadable files... [ 64%] data/tp53.json copying downloadable files... [ 68%] data/brca1-bats.fasta copying downloadable files... [ 72%] data/brca1.fasta copying downloadable files... [ 76%] data/GN-tree.json copying downloadable files... [ 80%] data/tree-with-support.json copying downloadable files... [ 84%] data/F9-demo.fa copying downloadable files... [ 88%] data/BRCA1-demo.fasta copying downloadable files... [ 92%] data/tbp.jaspar copying downloadable files... [ 96%] data/stats.tsv copying downloadable files... [100%] data/CerebellumDukeDNaseSeq.pk copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 858 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. rm -rf draw/ make[2]: Leaving directory '/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/doc' # remove superfluous files and dirs find doc/_build -name "*.doctree*" -delete rm -f doc/_build/html/_sources/COGENT_LICENSE.txt rm -f doc/_build/html/_static/jquery.js rm -f doc/_build/html/_static/underscore.js rm -rf doc/_build/html/_images/math/ make[1]: Leaving directory '/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg' dh: command-omitted: The call to "dh_auto_test -i -O--buildsystem=pybuild" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -i -O--buildsystem=pybuild dh_prep -i -O--buildsystem=pybuild dh_auto_install -i -O--buildsystem=pybuild I: pybuild plugin_flit:66: Installing package /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/src/cogent3 -> /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/debian/python3-cogent3/usr/lib/python3.9/dist-packages/cogent3 I: pybuild plugin_flit:79: Writing dist-info /build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg/debian/python3-cogent3/usr/lib/python3.9/dist-packages dh_install -i -O--buildsystem=pybuild debian/rules override_dh_installdocs make[1]: Entering directory '/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg' dh_installdocs rm -rf debian/python-cogent/usr/share/doc/python-cogent/html/_sources find debian -name doctrees -type d | xargs rm -rf make[1]: Leaving directory '/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg' dh_installchangelogs -i -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg' dh_python3 --shebang=/usr/bin/python3 I: dh_python3 pydist:235: Cannot find package that provides jupyterlab. Please add package that provides it to Build-Depends or add "jupyterlab python3-jupyterlab" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. I: dh_python3 pydist:235: Cannot find package that provides jupytext. Please add package that provides it to Build-Depends or add "jupytext python3-jupytext" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. I: dh_python3 pydist:235: Cannot find package that provides kaleido. Please add package that provides it to Build-Depends or add "kaleido python3-kaleido" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. I: dh_python3 pydist:235: Cannot find package that provides sphinx_panels. Please add package that provides it to Build-Depends or add "sphinx_panels python3-sphinx-panels" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. I: dh_python3 pydist:235: Cannot find package that provides jupyterlab. Please add package that provides it to Build-Depends or add "jupyterlab python3-jupyterlab" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. I: dh_python3 pydist:235: Cannot find package that provides jupytext. Please add package that provides it to Build-Depends or add "jupytext python3-jupytext" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. I: dh_python3 pydist:235: Cannot find package that provides kaleido. Please add package that provides it to Build-Depends or add "kaleido python3-kaleido" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. I: dh_python3 pydist:235: Cannot find package that provides sphinx_panels. Please add package that provides it to Build-Depends or add "sphinx_panels python3-sphinx-panels" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. I: dh_python3 pydist:235: Cannot find package that provides kaleido. Please add package that provides it to Build-Depends or add "kaleido python3-kaleido" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. make[1]: Leaving directory '/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg' dh_installsystemduser -i -O--buildsystem=pybuild dh_perl -i -O--buildsystem=pybuild dh_link -i -O--buildsystem=pybuild dh_strip_nondeterminism -i -O--buildsystem=pybuild debian/rules override_dh_compress make[1]: Entering directory '/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg' dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb make[1]: Leaving directory '/build/python-cogent-zLCQYQ/python-cogent-2021.10.12a1+dfsg' dh_fixperms -i -O--buildsystem=pybuild dh_missing -i -O--buildsystem=pybuild dh_installdeb -i -O--buildsystem=pybuild dh_gencontrol -i -O--buildsystem=pybuild dh_md5sums -i -O--buildsystem=pybuild dh_builddeb -i -O--buildsystem=pybuild dpkg-deb: building package 'python-cogent-doc' in '../python-cogent-doc_2021.10.12a1+dfsg-1_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../python-cogent_2021.10.12a1+dfsg-1_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/python-cogent-zLCQYQ /tmp/python-cogent-2021.10.12a1+dfsg-11053bbjh I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.iZ1LuJvRjE... I: success in 711.3437 seconds md5: Value of 'md5' differs for python-cogent-doc_2021.10.12a1+dfsg-1_all.deb md5: Size differs for python-cogent-doc_2021.10.12a1+dfsg-1_all.deb sha1: Value of 'sha1' differs for python-cogent-doc_2021.10.12a1+dfsg-1_all.deb sha1: Size differs for python-cogent-doc_2021.10.12a1+dfsg-1_all.deb sha256: Value of 'sha256' differs for python-cogent-doc_2021.10.12a1+dfsg-1_all.deb sha256: Size differs for python-cogent-doc_2021.10.12a1+dfsg-1_all.deb Checksums: FAIL Cannot generate diffoscope for python-cogent-doc_2021.10.12a1+dfsg-1_all.deb: RetryError[]